The 66 species of native wild mammals in West Virginia represent seven of the 10 orders of mammals found in North America. Most West Virginia species have a nearly statewide distribution, and are survivors from wildlife common to the wide area of the eastern deciduous forests present when the settlers arrived. A few other species—the northern water shrew, northern flying squirrel, snowshoe hare, Appalachian cottontail, rock vole, red-backed vole, and woodland deer mouse—are boreal or northern relicts, left behind when the northern forest retreated to isolated high elevations following the Ice Age. Except for the red backed vole and deer mouse, all boreals are uncommon and occur only in the high Allegheny mountains of eastern West Virginia. Three other uncommon species, the spotted skunk, Rafinesque's big eared bat, and golden mouse, are part of a southern fauna and reach their northern limits in southern West Virginia. The prairie vole, our only small mammal of Midwestern origin, has spread eastward across the Ohio River into the state. Several native species present in the early days were eliminated, including the mountain lion, porcupine, bison, elk, gray wolf, and coyote.

Three non-native or exotic species have become established. These are the Norway rat and the house mouse, which probably arrived with the earliest European settlers, and the European wild boar, released by the Department of Natural Resources in 1971 as a game species for reclaimed surface mines. Boar populations now exist in Boone, Logan, Raleigh, and Wyoming counties. Rats and mice are abundant throughout the state, frequently inhabiting fields and stream side habitats distant from dwellings. The roof rat or black rat, the first exotic rodent to reach West Virginia, has been replaced by the more aggressive Norway rat and is considered extinct in our region.

West Virginia is home to two species of bats protected by the federal Endangered Species Act. They are the Virginia big-eared bat and the Indiana bat. Both bats live in the eastern counties, where they form large hibernation colonies in the many limestone caves of that area. Other rare mammals, listed as "species of special concern," include the northern water shrew, star-nosed mole, rock vole, meadow jumping mouse, and Appalachian cottontail.

Among the rabbits and hares, the eastern cottontail is the common species below 3,000 feet. The boreal Appalachian cottontail, a secretive, uncommon cottontail, is at home in dense heath thickets among spruce and other conifers at the high elevations of the Alleghenies. A relatively good population exists in Dolly Sods. Declining numbers of the Appalachian cottontail are attributed to habitat destruction and fragmentation and invasions of the more adaptable and competitive eastern cottontail. The spectacular snowshoe hare is restricted to the high elevations in the eastern counties.

Rodents make up a significant proportion of the state's small mammals, both in numbers of individuals and numbers of species. Our only native rat, the Allegheny wood rat, lives in caves and rock crevices of the deciduous woodlands and is relatively common throughout much of the state. The abundant white-footed mouse is found statewide and is easily recognized by the golden wash of its fur. A relative, the deer mouse, has large ears and eyes and inhabits woodlands of the eastern mountains. A related but distinctly different kind of deer mouse is the smaller, small-eared, and short-tailed prairie deer mouse. Its habitat is fields in counties bordering the Ohio River. A very small brown mouse, the harvest mouse, is a seed-eater that nests above the ground in tall grass and is near the northern limits of its range in West Virginia.

Among the voles, another group of small rodents, the meadow vole is the herbivorous, common "field mouse" statewide. Its rare relative, the rock vole, was first discovered by scientists in Cranberry Glades during early explorations of the mountains. Populations of the rock vole are declining as the more aggressive meadow vole invades the higher elevations, and as its cool, moss-covered rock and woodland glades habitat dries from global warming. The red-backed vole, although a boreal species, has adapted to become the most common vole in the mountain forests, occupying the cool forests and extending southward along the north sides of the mountains into Fayette, Raleigh, and Mercer counties. The prairie vole, found in drier fields of counties along the Ohio River, is relatively common even though at the eastern edge of its range.

The eight species of shrews found in West Virginia, together with their relatives the moles, play a big role in keeping forest and agricultural pests under control. These small predators are poorly known, even though their total number is enormous. The shrews' high metabolic rate drives their round-the-clock search for grubs, insect larvae, worms, spiders, and other soil invertebrates. The short-tailed shrew is ubiquitous and probably our most abundant mammal. This shrew, often mistaken for a mole, is known to prey on baby mice, voles, and smaller shrews as well. Its relative, the least shrew, a very small brownish short-tailed shrew of old field habitat, is rare. Even smaller shrews include the masked, the smoky, and the tiny pygmy shrew. The pygmy shrew, unknown in the state until reported in 1986 from Canaan Valley, was later found to be widespread. The southeastern and northern water shrews are quite rare.

The beaver, our largest rodent, was exterminated soon after first settlement but reintroduced in the 1930s. They now occur throughout most of the state wherever there are small streams near deciduous woodlands, and in some areas have become a nuisance. Mammals helped by the wetland conditions created by beaver dams include raccoons, muskrats, and mink.

Among the carnivores, two native species, the fisher and the river otter, were exterminated and subsequently reintroduced as game species. In the mid-1800s, the fisher, a large weasel often referred to as "black fox," was fairly common in the spruce forests, but populations declined rapidly, first from trapping, then by habitat destruction. Reintroduced in the 1960s with 23 individuals from New Hampshire, the species has made a modest comeback with reforestation and a decline in trapping for fur. The river otter was abundant in most streams in 1925 but exterminated by the 1930s. Transplants of river otters from southern states into the Little Kanawha and West Fork rivers in the 1980s have shown modest success.

Large predators form the most notable gap among West Virginia wildlife. Bounties were paid for gray wolves until about 1822, and the species was exterminated by 1900. Mountain lions steadily declined in numbers and were declared extinct in 1924. Logging operations accompanied by road building and settlements steadily reduced the habitat for this large solitary cat. Predation on livestock and the decrease in deer population ensured its demise. Unconfirmed reports of this native predator are common, but there is no evidence to verify the continued presence of mountain lions in West Virginia. On the other hand, the shy and seldom seen bobcat, which subsists on smaller game, is relatively common in large wooded tracts in the state.

Today's largest mammalian predator is the coyote, a recent newcomer. This native species was quickly extirpated by the early European settlers but returned in recent years. Following the demise of large predators and over-population of managed game species, the coyote moved in to fill the vacant large predator niche. The species appears to have invaded primarily from the Midwest through Ohio and Kentucky. The coyote depends for food mostly upon medium and small prey—young turkeys, cottontails, and voles. Deer carrion from highway road kills or field dressing also is an important source of food. Coyotes sometimes hybridize with dogs producing "coy dogs." The abundance of feral dogs in the state, along with coyotes and hybrids, is a growing problem to suburbanites and farmers.

Black bear populations declined as timbering reduced habitat and poaching was uncontrolled. Management of the bear as a game species and regrowth of the forests have led to today's relative abundance of bears.

At the time of settlement of the area that was to become West Virginia, mammals were abundant and provided meat for the table and fur to use and sell. Clearing land for farming and the extensive timbering of the forests greatly reduced habitats for many species. Native deer, elk, bear, bison, mountain lion, fisher, otter, and rabbit populations were reduced dramatically, and all but bear, deer, and rabbit were extirpated. All except the bison and mountain lion have been reintroduced, and while elks apparently have entered the state from neighboring Kentucky, state wildlife officials begin a stocking program in December 2016 to encourage population growth. Continuing human endeavors such as surface mining, filling, draining, and redirecting streams, development of farm lands into subdivisions occupied by growing numbers of people and their pets, and proliferation of roads, power lines, and shopping malls, have changed forever the distribution, habitats, and populations of the mammals of the state.